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“We Are What We Eat”: How Diet Impacts the Gut Microbiota in Adulthood

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How Fermented Foods Feed a Healthy Gut Microbiota

Abstract

The important role of the microbes residing in our gut, collectively called the microbiota, in human health is widely acknowledged. There are numerous factors that have an impact on the microbiota in the gut of which diet is considered a crucial one. In this chapter we highlight our current knowledge on the ecology of the microbiota in adults and how it is affected by diet. We summarize observations from different cross-sectional and intervention studies that focused on the impact of diet on microbiota composition and activity. Special attention is paid to which microbial metabolites can be produced in the gut; how these are affected by different dietary components such as carbohydrates, fat, and proteins; and how these are associated to human health. Finally, we provide recommendations for future intervention studies in order to improve our understanding of the complex interplay between microbes, diet, and ourselves.

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References

  • Albenberg, L., Esipova, T. V., Judge, C. P., Bittinger, K., Chen, J., Laughlin, A., Grunberg, S., Baldassano, R. N., Lewis, J. D., & Li, H. (2014). Correlation between intraluminal oxygen gradient and radial partitioning of intestinal microbiota. Gastroenterology, 147(5), 1055–1063. e1058.

    Article  PubMed  Google Scholar 

  • An, R., Wilms, E., Masclee, A. A., Smidt, H., Zoetendal, E. G., & Jonkers, D. (2018). Age-dependent changes in GI physiology and microbiota: Time to reconsider? Gut, 67(12), 2213–2222.

    Article  CAS  PubMed  Google Scholar 

  • Arumugam, M., Raes, J., Pelletier, E., Le Paslier, D., Yamada, T., Mende, D. R., Fernandes, G. R., Tap, J., Bruls, T., Batto, J.-M., Bertalan, M., Borruel, N., Casellas, F., Fernandez, L., Gautier, L., Hansen, T., Hattori, M., Hayashi, T., Kleerebezem, M., Kurokawa, K., Leclerc, M., Levenez, F., Manichanh, C., Nielsen, H. B., Nielsen, T., Pons, N., Poulain, J., Qin, J., Sicheritz-Ponten, T., Tims, S., Torrents, D., Ugarte, E., Zoetendal, E. G., Wang, J., Guarner, F., Pedersen, O., de Vos, W. M., Brunak, S., Dore, J., Weissenbach, J., Ehrlich, S. D., Bork, P., & Meta, H. I. T. C. (2011). Enterotypes of the human gut microbiome. Nature, 473(7346), 174–180.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Atuma, C., Strugala, V., Allen, A., & Holm, L. (2001). The adherent gastrointestinal mucus gel layer: Thickness and physical state in vivo. American Journal of Physiology-Gastrointestinal and Liver Physiology, 280(5), G922–G929.

    Article  CAS  PubMed  Google Scholar 

  • Azcárate-Peril, M. A., Sikes, M., & Bruno-Bárcena, J. M. (2011). The intestinal microbiota, gastrointestinal environment and colorectal cancer: A putative role for probiotics in prevention of colorectal cancer? American Journal of Physiology-Gastrointestinal and Liver Physiology, 301(3), G401–G424.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Bashiardes, S., Godneva, A., Elinav, E., & Segal, E. (2018). Towards utilization of the human genome and microbiome for personalized nutrition. Current Opinion in Biotechnology, 51, 57–63.

    Article  CAS  PubMed  Google Scholar 

  • Begley, M., Gahan, C. G., & Hill, C. (2005). The interaction between bacteria and bile. FEMS Microbiology Reviews, 29(4), 625–651.

    Article  CAS  PubMed  Google Scholar 

  • Bonder, M. J., Tigchelaar, E. F., Cai, X., Trynka, G., Cenit, M. C., Hrdlickova, B., Zhong, H., Vatanen, T., Gevers, D., Wijmenga, C., Wang, Y., & Zhernakova, A. (2016). The influence of a short-term gluten-free diet on the human gut microbiome. Genome Medicine, 8(1), 45.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Booijink, C. C., El-Aidy, S., Rajilić-Stojanović, M., Heilig, H. G., Troost, F. J., Smidt, H., Kleerebezem, M., De Vos, W. M., & Zoetendal, E. G. (2010). High temporal and inter-individual variation detected in the human ileal microbiota. Environmental Microbiology, 12(12), 3213–3227.

    Article  CAS  PubMed  Google Scholar 

  • Bui, T. P. N., Ritari, J., Boeren, S., De Waard, P., Plugge, C. M., & De Vos, W. M. (2015). Production of butyrate from lysine and the Amadori product fructoselysine by a human gut commensal. Nature Communications, 6, 10062.

    Article  CAS  PubMed  Google Scholar 

  • Canfora, E. E., van der Beek, C. M., Hermes, G. D., Goossens, G. H., Jocken, J. W., Holst, J. J., van Eijk, H. M., Venema, K., Smidt, H., & Zoetendal, E. G. (2017). Supplementation of diet with galacto-oligosaccharides increases bifidobacteria, but not insulin sensitivity, in obese prediabetic individuals. Gastroenterology, 153(1), 87–97.

    Article  CAS  PubMed  Google Scholar 

  • Carbonero, F., Benefiel, A. C., & Gaskins, H. R. (2012). Contributions of the microbial hydrogen economy to colonic homeostasis. Nature Reviews. Gastroenterology & Hepatology, 9(9), 504–518.

    Article  CAS  Google Scholar 

  • Cheng, J., Ringel-Kulka, T., Heikamp-de Jong, I., Ringel, Y., Carroll, I., De Vos, W. M., Salojärvi, J., & Satokari, R. (2016). Discordant temporal development of bacterial phyla and the emergence of core in the fecal microbiota of young children. The ISME Journal, 10(4), 1002–1014.

    Article  PubMed  Google Scholar 

  • Conlon, M. A., & Bird, A. R. (2014). The impact of diet and lifestyle on gut microbiota and human health. Nutrients, 7(1), 17–44.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Costabile, A., Klinder, A., Fava, F., Napolitano, A., Fogliano, V., Leonard, C., Gibson, G. R., & Tuohy, K. M. (2008). Whole-grain wheat breakfast cereal has a prebiotic effect on the human gut microbiota: A double-blind, placebo-controlled, crossover study. British Journal of Nutrition, 99(1), 110–120.

    Article  CAS  PubMed  Google Scholar 

  • Costabile, A., Kolida, S., Klinder, A., Gietl, E., Bäuerlein, M., Frohberg, C., Landschütze, V., & Gibson, G. R. (2010). A double-blind, placebo-controlled, cross-over study to establish the bifidogenic effect of a very-long-chain inulin extracted from globe artichoke (Cynara scolymus) in healthy human subjects. British Journal of Nutrition, 104(7), 1007–1017.

    Article  CAS  PubMed  Google Scholar 

  • Costea, P. I., Hildebrand, F., Manimozhiyan, A., Bäckhed, F., Blaser, M. J., Bushman, F. D., De Vos, W. M., Ehrlich, S. D., Fraser, C. M., & Hattori, M. (2018). Enterotypes in the landscape of gut microbial community composition. Nature Microbiology, 3(1), 8.

    Article  CAS  PubMed  Google Scholar 

  • Cummings, J., Pomare, E., Branch, W., Naylor, C., & Macfarlane, G. (1987). Short chain fatty acids in human large intestine, portal, hepatic and venous blood. Gut, 28(10), 1221–1227.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • David, L. A., Maurice, C. F., Carmody, R. N., Gootenberg, D. B., Button, J. E., Wolfe, B. E., Ling, A. V., Devlin, A. S., Varma, Y., Fischbach, M. A., Biddinger, S. B., Dutton, R. J., & Turnbaugh, P. J. (2014). Diet rapidly and reproducibly alters the human gut microbiome. Nature, 505(7484), 559.

    Article  CAS  PubMed  Google Scholar 

  • De Filippis, F., Pellegrini, N., Vannini, L., Jeffery, I. B., La Storia, A., Laghi, L., Serrazanetti, D. I., Di Cagno, R., Ferrocino, I., & Lazzi, C. (2016). High-level adherence to a Mediterranean diet beneficially impacts the gut microbiota and associated metabolome. Gut, 65(11), 1812–1821.

    Article  PubMed  CAS  Google Scholar 

  • De Filippo, C., Cavalieri, D., Di Paola, M., Ramazzotti, M., Poullet, J. B., Massart, S., Collini, S., Pieraccini, G., & Lionetti, P. (2010). Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proceedings of the National Academy of Sciences, 107(33), 14691–14696.

    Article  Google Scholar 

  • De Filippo, C., Di Paola, M., Ramazzotti, M., Albanese, D., Pieraccini, G., Banci, E., Miglietta, F., Cavalieri, D., & Lionetti, P. (2017). Diet, environments, and gut microbiota. a preliminary investigation in children living in rural and urban burkina faso and italy. Frontiers in Microbiology, 8, 1979.

    Article  PubMed  PubMed Central  Google Scholar 

  • De Palma, G., Nadal, I., Carmen Collado, M., & Sanz, Y. (2009). Effects of a gluten-free diet on gut microbiota and immune function in healthy adult human subjects. British Journal of Nutrition, 102(8), 1154–1160.

    Article  PubMed  CAS  Google Scholar 

  • de Vos, W. M. (2017). Microbe profile: Akkermansia muciniphila: A conserved intestinal symbiont that acts as the gatekeeper of our mucosa. Microbiology, 163(5), 646–648.

    Article  PubMed  CAS  Google Scholar 

  • Derrien, M., Vaughan, E. E., Plugge, C. M., & de Vos, W. M. (2004). Akkermansia muciniphila gen. nov., sp. nov., a human intestinal mucin-degrading bacterium. International Journal of Systematic and Evolutionary Microbiology, 54(5), 1469–1476.

    Article  CAS  PubMed  Google Scholar 

  • Dewulf, E. M., Cani, P. D., Claus, S. P., Fuentes, S., Puylaert, P. G., Neyrinck, A. M., Bindels, L. B., de Vos, W. M., Gibson, G. R., & Thissen, J.-P. (2013). Insight into the prebiotic concept: Lessons from an exploratory, double blind intervention study with inulin-type fructans in obese women. Gut, 62(8), 1112–1121.

    Article  CAS  PubMed  Google Scholar 

  • Donaldson, G. P., Lee, S. M., & Mazmanian, S. K. (2016). Gut biogeography of the bacterial microbiota. Nature Reviews Microbiology, 14(1), 20–32.

    Article  CAS  PubMed  Google Scholar 

  • Donia, M. S., & Fischbach, M. A. (2015). Small molecules from the human microbiota. Science, 349(6246), 1254766.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Duncan, S. H., Lobley, G., Holtrop, G., Ince, J., Johnstone, A., Louis, P., & Flint, H. J. (2008). Human colonic microbiota associated with diet, obesity and weight loss. International Journal of Obesity, 32(11), 1720.

    Article  CAS  PubMed  Google Scholar 

  • Duncan, S. H., Louis, P., Thomson, J. M., & Flint, H. J. (2009). The role of pH in determining the species composition of the human colonic microbiota. Environmental Microbiology, 11(8), 2112–2122.

    Article  PubMed  Google Scholar 

  • Elzinga, J., van der Oost, J., de Vos, W. M., & Smidt, H. (2019). The use of defined microbial communities to model host-microbe interactions in the human gut. Microbiology and Molecular Biology Reviews, 83(2), e00054–e00018.

    Article  PubMed  PubMed Central  Google Scholar 

  • Falony, G., Joossens, M., Vieira-Silva, S., Wang, J., Darzi, Y., Faust, K., Kurilshikov, A., Bonder, M. J., Valles-Colomer, M., & Vandeputte, D. (2016). Population-level analysis of gut microbiome variation. Science, 352(6285), 560–564.

    Article  CAS  PubMed  Google Scholar 

  • Fava, F., Gitau, R., Griffin, B., Gibson, G., Tuohy, K., & Lovegrove, J. (2013). The type and quantity of dietary fat and carbohydrate alter faecal microbiome and short-chain fatty acid excretion in a metabolic syndrome ‘at-risk’ population. International Journal of Obesity, 37(2), 216.

    Article  CAS  PubMed  Google Scholar 

  • Feng, Y., Stams, A. J., De Vos, W. M., & Sánchez-Andrea, I. (2017). Enrichment of sulfidogenic bacteria from the human intestinal tract. FEMS Microbiology Letters, 364(4), fnx028.

    Article  CAS  Google Scholar 

  • Foerster, J., Maskarinec, G., Reichardt, N., Tett, A., Narbad, A., Blaut, M., & Boeing, H. (2014). The influence of whole grain products and red meat on intestinal microbiota composition in normal weight adults: A randomized crossover intervention trial. PLoS One, 9(10), e109606.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Frank, D. N., Amand, A. L. S., Feldman, R. A., Boedeker, E. C., Harpaz, N., & Pace, N. R. (2007). Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proceedings of the National Academy of Sciences, 104(34), 13780–13785.

    Article  CAS  Google Scholar 

  • Fuentes, S., Rossen, N. G., van der Spek, M. J., Hartman, J. H., Huuskonen, L., Korpela, K., Salojärvi, J., Aalvink, S., de Vos, W. M., & D’Haens, G. R. (2017). Microbial shifts and signatures of long-term remission in ulcerative colitis after faecal microbiota transplantation. The ISME Journal, 11(8), 1877.

    Article  PubMed  PubMed Central  Google Scholar 

  • Geerlings, S., Kostopoulos, I., de Vos, W., & Belzer, C. (2018). Akkermansia muciniphila in the human gastrointestinal tract: When, where, and how? Microorganisms, 6(3), 75.

    Article  CAS  PubMed Central  Google Scholar 

  • Goodrich, J. K., Waters, J. L., Poole, A. C., Sutter, J. L., Koren, O., Blekhman, R., Beaumont, M., Van Treuren, W., Knight, R., & Bell, J. T. (2014). Human genetics shape the gut microbiome. Cell, 159(4), 789–799.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hald, S., Schioldan, A. G., Moore, M. E., Dige, A., Lærke, H. N., Agnholt, J., Knudsen, K. E. B., Hermansen, K., Marco, M. L., & Gregersen, S. (2016). Effects of arabinoxylan and resistant starch on intestinal microbiota and short-chain fatty acids in subjects with metabolic syndrome: A randomised crossover study. PLoS One, 11(7), e0159223.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Halmos, E. P., Christophersen, C. T., Bird, A. R., Shepherd, S. J., Gibson, P. R., & Muir, J. G. (2014a). Diets that differ in their FODMAP content alter the colonic luminal microenvironment. Gut, 64(1), 93–100.

    Article  PubMed  CAS  Google Scholar 

  • Halmos, E. P., Power, V. A., Shepherd, S. J., Gibson, P. R., & Muir, J. G. (2014b). A diet low in FODMAPs reduces symptoms of irritable bowel syndrome. Gastroenterology, 146(1), 67–75. e65.

    Article  CAS  PubMed  Google Scholar 

  • Henning, S. M., Yang, J., Shao, P., Lee, R.-P., Huang, J., Ly, A., Hsu, M., Lu, Q.-Y., Thames, G., & Heber, D. (2017). Health benefit of vegetable/fruit juice-based diet: Role of microbiome. Scientific Reports, 7(1), 2167.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Hermes, G. (2016). Mining the human intestinal microbiota for biomarkers associated with metabolic disorders. Ph.D. thesis, Wageningen University.

    Google Scholar 

  • Islam, K. S., Fukiya, S., Hagio, M., Fujii, N., Ishizuka, S., Ooka, T., Ogura, Y., Hayashi, T., & Yokota, A. (2011). Bile acid is a host factor that regulates the composition of the cecal microbiota in rats. Gastroenterology, 141(5), 1773–1781.

    Article  CAS  PubMed  Google Scholar 

  • Jantchou, P., Morois, S., Clavel-Chapelon, F., Boutron-Ruault, M.-C., & Carbonnel, F. (2010). Animal protein intake and risk of inflammatory bowel disease: The E3N prospective study. The American Journal of Gastroenterology, 105(10), 2195.

    Article  CAS  PubMed  Google Scholar 

  • Jones, B. V., Begley, M., Hill, C., Gahan, C. G., & Marchesi, J. R. (2008). Functional and comparative metagenomic analysis of bile salt hydrolase activity in the human gut microbiome. Proceedings of the National Academy of Sciences, 105(36), 13580–13585.

    Article  CAS  Google Scholar 

  • Jones, R. B., Zhu, X. Z., Moan, E., Murff, H. J., Ness, R. M., Seidner, D. L., Sun, S., Yu, C., Dai, Q., Fodor, A. A., Azcarate-Peril, M. A., & Shrubsole, M. J. (2018). Inter-niche and inter-individual variation in gut microbial community assessment using stool, rectal swab, and mucosal samples. Scientific Reports, 8(1), 4139.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Kashyap, P. C., Marcobal, A., Ursell, L. K., Larauche, M., Duboc, H., Earle, K. A., Sonnenburg, E. D., Ferreyra, J. A., Higginbottom, S. K., & Million, M. (2013). Complex interactions among diet, gastrointestinal transit, and gut microbiota in humanized mice. Gastroenterology, 144(5), 967–977.

    Article  PubMed  Google Scholar 

  • Kau, A. L., Ahern, P. P., Griffin, N. W., Goodman, A. L., & Gordon, J. I. (2011). Human nutrition, the gut microbiome and the immune system. Nature, 474(7351), 327–336.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Koh, A., De Vadder, F., Kovatcheva-Datchary, P., & Bäckhed, F. (2016). From dietary fiber to host physiology: Short-chain fatty acids as key bacterial metabolites. Cell, 165(6), 1332–1345.

    Article  CAS  PubMed  Google Scholar 

  • Korpela, K., Flint, H. J., Johnstone, A. M., Lappi, J., Poutanen, K., Dewulf, E., Delzenne, N., De Vos, W. M., & Salonen, A. (2014). Gut microbiota signatures predict host and microbiota responses to dietary interventions in obese individuals. PLoS One, 9(3), e90702.

    Article  PubMed  PubMed Central  Google Scholar 

  • Kovatcheva-Datchary, P., Nilsson, A., Akrami, R., Lee, Y. S., De Vadder, F., Arora, T., Hallen, A., Martens, E., Bjorck, I., & Backhed, F. (2015). Dietary fiber-induced improvement in glucose metabolism is associated with increased abundance of Prevotella. Cell Metabolism, 22(6), 971–982.

    Article  CAS  PubMed  Google Scholar 

  • Lahti, L., Salojärvi, J., Salonen, A., Scheffer, M., & De Vos, W. M. (2014). Tipping elements in the human intestinal ecosystem. Nature Communications, 5, 4344.

    Article  CAS  PubMed  Google Scholar 

  • Lappi, J., Salojärvi, J., Kolehmainen, M., Mykkänen, H., Poutanen, K., de Vos, W. M., & Salonen, A. (2013). Intake of whole-grain and fiber-rich rye bread versus refined wheat bread does not differentiate intestinal microbiota composition in Finnish adults with metabolic syndrome. The Journal of Nutrition, 143(5), 648–655.

    Article  CAS  PubMed  Google Scholar 

  • Larsen, N., Vogensen, F. K., van den Berg, F. W., Nielsen, D. S., Andreasen, A. S., Pedersen, B. K., Al-Soud, W. A., Sørensen, S. J., Hansen, L. H., & Jakobsen, M. (2010). Gut microbiota in human adults with type 2 diabetes differs from non-diabetic adults. PLoS One, 5(2), e9085.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Le Chatelier, E., Nielsen, T., Qin, J., Prifti, E., Hildebrand, F., Falony, G., Almeida, M., Arumugam, M., Batto, J.-M., & Kennedy, S. (2013). Richness of human gut microbiome correlates with metabolic markers. Nature, 500(7464), 541.

    Article  PubMed  CAS  Google Scholar 

  • Lepage, P., Seksik, P., Sutren, M., de la Cochetiere, M.-F., Jian, R., Marteau, P., & Doré, J. (2005). Biodiversity of the mucosa-associated microbiota is stable along the distal digestive tract in healthy individuals and patients with IBD. Inflammatory Bowel Diseases, 11(5), 473–480.

    Article  PubMed  Google Scholar 

  • Levitt, M. D., Furne, J. K., Kuskowski, M., & Ruddy, J. (2006). Stability of human methanogenic flora over 35 years and a review of insights obtained from breath methane measurements. Clinical Gastroenterology and Hepatology, 4(2), 123–129.

    Article  CAS  PubMed  Google Scholar 

  • Ley, R. E., Turnbaugh, P. J., Klein, S., & Gordon, J. I. (2006). Microbial ecology: Human gut microbes associated with obesity. Nature, 444(7122), 1022–1023.

    Article  CAS  PubMed  Google Scholar 

  • Li, J., Jia, H., Cai, X., Zhong, H., Feng, Q., Sunagawa, S., Arumugam, M., Kultima, J. R., Prifti, E., & Nielsen, T. (2014). An integrated catalog of reference genes in the human gut microbiome. Nature Biotechnology, 32(8), 834.

    Article  CAS  PubMed  Google Scholar 

  • Lin, S. H., Chou, L. M., Chien, Y. W., Chang, J. S., & Lin, C. I. (2016). Prebiotic effects of xylooligosaccharides on the improvement of microbiota balance in human subjects. Gastroenterology Research and Practice, 2016(2016), 5789232.

    PubMed  PubMed Central  Google Scholar 

  • Liu, F., Li, P., Chen, M., Luo, Y., Prabhakar, M., Zheng, H., He, Y., Qi, Q., Long, H., & Zhang, Y. (2017). Fructooligosaccharide (FOS) and galactooligosaccharide (GOS) increase bifidobacterium but reduce butyrate producing bacteria with adverse glycemic metabolism in healthy young population. Scientific Reports, 7(1), 11789.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Louis, P., Hold, G. L., & Flint, H. J. (2014). The gut microbiota, bacterial metabolites and colorectal cancer. Nature Reviews Microbiology, 12(10), 661.

    Article  CAS  PubMed  Google Scholar 

  • Lozupone, C. A., Stombaugh, J. I., Gordon, J. I., Jansson, J. K., & Knight, R. (2012). Diversity, stability and resilience of the human gut microbiota. Nature, 489(7415), 220–230.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lynch, S. V., & Pedersen, O. (2016). The human intestinal microbiome in health and disease. New England Journal of Medicine, 375(24), 2369–2379.

    Article  CAS  PubMed  Google Scholar 

  • Macfarlane, G., Cummings, J., & Allison, C. (1986). Protein degradation by human intestinal bacteria. Microbiology, 132(6), 1647–1656.

    Article  CAS  Google Scholar 

  • Martinez, I., Lattimer, J. M., Hubach, K. L., Case, J. A., Yang, J., Weber, C. G., Louk, J. A., Rose, D. J., Kyureghian, G., Peterson, D. A., Haub, M. D., & Walter, J. (2013). Gut microbiome composition is linked to whole grain-induced immunological improvements. ISME Journal, 7(2), 269–280.

    Article  CAS  PubMed  Google Scholar 

  • Maslowski, K. M., & Mackay, C. R. (2011). Diet, gut microbiota and immune responses. Nature Immunology, 12(1), 5–9.

    Article  CAS  PubMed  Google Scholar 

  • Menni, C., Lin, C., Cecelja, M., Mangino, M., Matey-Hernandez, M. L., Keehn, L., Mohney, R. P., Steves, C. J., Spector, T. D., Kuo, C.-F., Chowienczyk, P., & Valdes, A. M. (2018). Gut microbial diversity is associated with lower arterial stiffness in women. European Heart Journal, 39(25), 2390–2397.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Miller, T. L., & Wolin, M. J. (1996). Pathways of acetate, propionate, and butyrate formation by the human fecal microbial flora. Applied and Environmental Microbiology, 62(5), 1589–1592.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Moayyedi, P., Surette, M. G., Kim, P. T., Libertucci, J., Wolfe, M., Onischi, C., Armstrong, D., Marshall, J. K., Kassam, Z., & Reinisch, W. (2015). Fecal microbiota transplantation induces remission in patients with active ulcerative colitis in a randomized controlled trial. Gastroenterology, 149(1), 102–109. e106.

    Article  PubMed  Google Scholar 

  • Nakamura, N., Lin, H. C., McSweeney, C. S., Mackie, R. I., & Gaskins, H. R. (2010). Mechanisms of microbial hydrogen disposal in the human colon and implications for health and disease. Annual Review of Food Science and Technology, 1, 363–395.

    Article  CAS  PubMed  Google Scholar 

  • Nicholson, J. K., Holmes, E., Kinross, J., Burcelin, R., Gibson, G., Jia, W., & Pettersson, S. (2012). Host-gut microbiota metabolic interactions. Science, 336(6086), 1262–1267.

    Article  CAS  PubMed  Google Scholar 

  • Nyangale, E. P., Mottram, D. S., & Gibson, G. R. (2012). Gut microbial activity, implications for health and disease: The potential role of metabolite analysis. Journal of Proteome Research, 11(12), 5573–5585.

    Article  CAS  PubMed  Google Scholar 

  • O’Keefe, S. J., Li, J. V., Lahti, L., Ou, J., Carbonero, F., Mohammed, K., Posma, J. M., Kinross, J., Wahl, E., & Ruder, E. (2015). Fat, fibre and cancer risk in African Americans and rural Africans. Nature Communications, 6, 6342.

    Article  PubMed  CAS  Google Scholar 

  • O’Toole, P. W., & Jeffery, I. B. (2015). Gut microbiota and aging. Science, 350(6265), 1214–1215.

    Article  PubMed  CAS  Google Scholar 

  • Ott, B., Skurk, T., Lagkouvardos, L., Fischer, S., Büttner, J., Lichtenegger, M., Clavel, T., Lechner, A., Rychlik, M., & Haller, D. (2018). Short-term overfeeding with dairy cream does not modify gut permeability, the fecal microbiota, or glucose metabolism in young healthy men. The Journal of Nutrition, 148(1), 77–85.

    Article  PubMed  Google Scholar 

  • Ou, G., Hedberg, M., Hörstedt, P., Baranov, V., Forsberg, G., Drobni, M., Sandström, O., Wai, S. N., Johansson, I., & Hammarström, M.-L. (2009). Proximal small intestinal microbiota and identification of rod-shaped bacteria associated with childhood celiac disease. The American Journal of Gastroenterology, 104, 3058–3067.

    Article  PubMed  Google Scholar 

  • Ou, J., DeLany, J. P., Zhang, M., Sharma, S., & O’Keefe, S. J. (2012). Association between low colonic short-chain fatty acids and high bile acids in high colon cancer risk populations. Nutrition and Cancer, 64(1), 34–40.

    Article  CAS  PubMed  Google Scholar 

  • Ou, J., Carbonero, F., Zoetendal, E. G., DeLany, J. P., Wang, M., Newton, K., Gaskins, H. R., & O’keefe, S. J. (2013). Diet, microbiota, and microbial metabolites in colon cancer risk in rural Africans and African Americans. The American Journal of Clinical Nutrition, 98(1), 111–120.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pochart, P., Dore, J., Lemann, F., Goderel, I., & Rambaud, J. C. (1992). Interrelations between populations of methanogenic archaea and sulfate-reducing bacteria in the human colon. FEMS Microbiology Letters, 98(1–3), 225–228.

    Article  CAS  Google Scholar 

  • Qin, J. J., Li, R. Q., Raes, J., Arumugam, M., Burgdorf, K. S., Manichanh, C., Nielsen, T., Pons, N., Levenez, F., Yamada, T., Mende, D. R., Li, J. H., Xu, J. M., Li, S. C., Li, D. F., Cao, J. J., Wang, B., Liang, H. Q., Zheng, H. S., Xie, Y. L., Tap, J., Lepage, P., Bertalan, M., Batto, J. M., Hansen, T., Le Paslier, D., Linneberg, A., Nielsen, H. B., Pelletier, E., Renault, P., Sicheritz-Ponten, T., Turner, K., Zhu, H. M., Yu, C., Li, S. T., Jian, M., Zhou, Y., Li, Y. R., Zhang, X. Q., Li, S. G., Qin, N., Yang, H. M., Wang, J., Brunak, S., Dore, J., Guarner, F., Kristiansen, K., Pedersen, O., Parkhill, J., Weissenbach, J., Bork, P., Ehrlich, S. D., Wang, J., & Consortium, M. (2010). A human gut microbial gene catalogue established by metagenomic sequencing. Nature, 464(7285), 59–U70.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rajilić-Stojanović, M., Smidt, H., & De Vos, W. M. (2007). Diversity of the human gastrointestinal tract microbiota revisited. Environmental Microbiology, 9(9), 2125–2136.

    Article  PubMed  Google Scholar 

  • Rajilić-Stojanović, M., Heilig, H. G., Tims, S., Zoetendal, E. G., & Vos, W. M. (2013). Long-term monitoring of the human intestinal microbiota composition. Environmental Microbiology, 15(4), 1146–1159.

    Article  CAS  Google Scholar 

  • Reiss, A., Jacobi, M., Rusch, K., & Schwiertz, A. (2016). Association of dietary type with fecal microbiota and short chain fatty acids in vegans and omnivores. The Journal International Society of Microbiota, 2, 1.

    Google Scholar 

  • Rey, F. E., Faith, J. J., Bain, J., Muehlbauer, M. J., Stevens, R. D., Newgard, C. B., & Gordon, J. I. (2010). Dissecting the in vivo metabolic potential of two human gut acetogens. Journal of Biological Chemistry, 285(29), 22082–22090.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ridlon, J. M., Kang, D.-J., & Hylemon, P. B. (2006). Bile salt biotransformations by human intestinal bacteria. Journal of Lipid Research, 47(2), 241–259.

    Article  CAS  PubMed  Google Scholar 

  • Ridlon, J. M., Kang, D. J., Hylemon, P. B., & Bajaj, J. S. (2014). Bile acids and the gut microbiome. Current Opinion in Gastroenterology, 30(3), 332.

    Article  PubMed  PubMed Central  Google Scholar 

  • Roager, H. M., Vogt, J. K., Kristensen, M., Hansen, L. B. S., Ibrügger, S., Mærkedahl, R. B., Bahl, M. I., Lind, M. V., Nielsen, R. L., & Frøkiær, H. (2017). Whole grain-rich diet reduces body weight and systemic low-grade inflammation without inducing major changes of the gut microbiome: A randomised cross-over trial. Gut, 68(1), 83–93.

    Article  PubMed  CAS  Google Scholar 

  • Ross, A. B., Bruce, S. J., Blondel-Lubrano, A., Oguey-Araymon, S., Beaumont, M., Bourgeois, A., Nielsen-Moennoz, C., Vigo, M., Fay, L.-B., & Kochhar, S. (2011). A whole-grain cereal-rich diet increases plasma betaine, and tends to decrease total and LDL-cholesterol compared with a refined-grain diet in healthy subjects. British Journal of Nutrition, 105(10), 1492–1502.

    Article  CAS  PubMed  Google Scholar 

  • Rossen, N. G., Fuentes, S., van der Spek, M. J., Tijssen, J. G., Hartman, J. H., Duflou, A., Löwenberg, M., van den Brink, G. R., Mathus-Vliegen, E. M., & de Vos, W. M. (2015). Findings from a randomized controlled trial of fecal transplantation for patients with ulcerative colitis. Gastroenterology, 149(1), 110–118. e114.

    Article  PubMed  Google Scholar 

  • Russell, W. R., Gratz, S. W., Duncan, S. H., Holtrop, G., Ince, J., Scobbie, L., Duncan, G., Johnstone, A. M., Lobley, G. E., & Wallace, R. J. (2011). High-protein, reduced-carbohydrate weight-loss diets promote metabolite profiles likely to be detrimental to colonic health. The American Journal of Clinical Nutrition, 93(5), 1062–1072.

    Article  CAS  PubMed  Google Scholar 

  • Salonen, A., Lahti, L., Salojarvi, J., Holtrop, G., Korpela, K., Duncan, S. H., Date, P., Farquharson, F., Johnstone, A. M., Lobley, G. E., Louis, P., Flint, H. J., & de Vos, W. M. (2014). Impact of diet and individual variation on intestinal microbiota composition and fermentation products in obese men. ISME Journal, 8(11), 2218–2230.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Saresella, M., Mendozzi, L., Rossi, V., Mazzali, F., Piancone, F., LaRosa, F., Marventano, I., Caputo, D., Felis, G. E., & Clerici, M. (2017). Immunological and clinical effect of diet modulation of the gut microbiome in multiple sclerosis patients: A pilot study. Frontiers in Immunology, 8, 1391.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Schwiertz, A., Taras, D., Schaefer, K., Beijer, S., Bos, N. A., Donus, C., & Hardt, P. D. (2010). Microbiota and SCFA in lean and overweight healthy subjects. Obesity, 18(1), 190–195.

    Article  PubMed  Google Scholar 

  • Segal, I., Walker, A., Lord, S., & Cummings, J. (1988). Breath methane and large bowel cancer risk in contrasting African populations. Gut, 29(5), 608–613.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sender, R., Fuchs, S., & Milo, R. (2016a). Are we really vastly outnumbered? Revisiting the ratio of bacterial to host cells in humans. Cell, 164(3), 337–340.

    Article  CAS  PubMed  Google Scholar 

  • Sender, R., Fuchs, S., & Milo, R. (2016b). Revised estimates for the number of human and bacteria cells in the body. PLoS Biology, 14(8), e1002533.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Shetty, S. A., Hugenholtz, F., Lahti, L., Smidt, H., & de Vos, W. M. (2017). Intestinal microbiome landscaping: Insight in community assemblage and implications for microbial modulation strategies. FEMS Microbiology Reviews, 41(2), 182–199.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shetty, S. A., Smidt, H., & de Vos, W. M. (2019). Reconstructing functional networks in the human intestinal tract using synthetic microbiomes. Current Opinion in Biotechnology, 58, 146–154.

    Article  CAS  PubMed  Google Scholar 

  • Shoaie, S., Ghaffari, P., Kovatcheva-Datchary, P., Mardinoglu, A., Sen, P., Pujos-Guillot, E., de Wouters, T., Juste, C., Rizkalla, S., & Chilloux, J. (2015). Quantifying diet-induced metabolic changes of the human gut microbiome. Cell Metabolism, 22(2), 320–331.

    Article  CAS  PubMed  Google Scholar 

  • Sonnenburg, E. D., Smits, S. A., Tikhonov, M., Higginbottom, S. K., Wingreen, N. S., & Sonnenburg, J. L. (2016). Diet-induced extinctions in the gut microbiota compound over generations. Nature, 529(7585), 212–U208.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Stams, A. J., & Plugge, C. M. (2009). Electron transfer in syntrophic communities of anaerobic bacteria and archaea. Nature Reviews Microbiology, 7(8), 568.

    Article  CAS  PubMed  Google Scholar 

  • Staudacher, H. M., Lomer, M. C., Anderson, J. L., Barrett, J. S., Muir, J. G., Irving, P. M., & Whelan, K. (2012). Fermentable carbohydrate restriction reduces luminal bifidobacteria and gastrointestinal symptoms in patients with irritable bowel syndrome. The Journal of Nutrition, 142(8), 1510–1518.

    Article  CAS  PubMed  Google Scholar 

  • Tap, J., Furet, J. P., Bensaada, M., Philippe, C., Roth, H., Rabot, S., Lakhdari, O., Lombard, V., Henrissat, B., & Corthier, G. (2015). Gut microbiota richness promotes its stability upon increased dietary fibre intake in healthy adults. Environmental Microbiology, 17(12), 4954–4964.

    Article  CAS  PubMed  Google Scholar 

  • The Human Microbiome Project Consortium. (2012). Structure, function and diversity of the healthy human microbiome. Nature, 486(7402), 207–214.

    Article  PubMed Central  CAS  Google Scholar 

  • Tuohy, K., Kolida, S., Lustenberger, A., & Gibson, G. R. (2001). The prebiotic effects of biscuits containing partially hydrolysed guar gum and fructo-oligosaccharides—A human volunteer study. British Journal of Nutrition, 86(3), 341–348.

    Article  CAS  PubMed  Google Scholar 

  • Turnbaugh, P. J., Ley, R. E., Mahowald, M. A., Magrini, V., Mardis, E. R., & Gordon, J. I. (2006). An obesity-associated gut microbiome with increased capacity for energy harvest. Nature, 444(7122), 1027–1031.

    Article  PubMed  Google Scholar 

  • Van Nood, E., Vrieze, A., Nieuwdorp, M., Fuentes, S., Zoetendal, E. G., de Vos, W. M., Visser, C. E., Kuijper, E. J., Bartelsman, J. F., & Tijssen, J. G. (2013). Duodenal infusion of donor feces for recurrent Clostridium difficile. New England Journal of Medicine, 368(5), 407–415.

    Article  PubMed  CAS  Google Scholar 

  • Vandeputte, D., Falony, G., Vieira-Silva, S., Wang, J., Sailer, M., Theis, S., Verbeke, K., & Raes, J. (2017). Prebiotic inulin-type fructans induce specific changes in the human gut microbiota. Gut, 66(11), 1968–1974.

    Article  CAS  PubMed  Google Scholar 

  • Vermeire, S., Joossens, M., Verbeke, K., Wang, J., Machiels, K., Sabino, J., Ferrante, M., Van Assche, G., Rutgeerts, P., & Raes, J. (2016). Donor species richness determines faecal microbiota transplantation success in inflammatory bowel disease. Journal of Crohn’s and Colitis, 10(4), 387–394.

    Article  PubMed  Google Scholar 

  • Vital, M., Howe, A. C., & Tiedje, J. M. (2014). Revealing the bacterial butyrate synthesis pathways by analyzing (meta) genomic data. MBio, 5(2), e00889–e00814.

    Article  PubMed  PubMed Central  Google Scholar 

  • Vuholm, S., Nielsen, D. S., Iversen, K. N., Suhr, J., Westermann, P., Krych, L., Andersen, J. R., & Kristensen, M. (2017). Whole-grain rye and wheat affect some markers of gut health without altering the fecal microbiota in healthy overweight adults: A 6-week randomized trial. The Journal of Nutrition, 147(11), 2067–2075.

    CAS  PubMed  Google Scholar 

  • Walker, A. W., Ince, J., Duncan, S. H., Webster, L. M., Holtrop, G., Ze, X., Brown, D., Stares, M. D., Scott, P., & Bergerat, A. (2011). Dominant and diet-responsive groups of bacteria within the human colonic microbiota. The ISME Journal, 5(2), 220–230.

    Article  CAS  PubMed  Google Scholar 

  • Wang, T., Cai, G., Qiu, Y., Fei, N., Zhang, M., Pang, X., Jia, W., Cai, S., & Zhao, L. (2012). Structural segregation of gut microbiota between colorectal cancer patients and healthy volunteers. The ISME Journal, 6(2), 320–329.

    Article  CAS  PubMed  Google Scholar 

  • Windey, K., De Preter, V., Louat, T., Schuit, F., Herman, J., Vansant, G., & Verbeke, K. (2012a). Modulation of protein fermentation does not affect fecal water toxicity: A randomized cross-over study in healthy subjects. PLoS One, 7(12), e52387.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Windey, K., De Preter, V., & Verbeke, K. (2012b). Relevance of protein fermentation to gut health. Molecular Nutrition & Food Research, 56(1), 184–196.

    Article  CAS  Google Scholar 

  • Wu, G. D., Chen, J., Hoffmann, C., Bittinger, K., Chen, Y.-Y., Keilbaugh, S. A., Bewtra, M., Knights, D., Walters, W. A., & Knight, R. (2011). Linking long-term dietary patterns with gut microbial enterotypes. Science, 334(6052), 105–108.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Xiao, S., Fei, N., Pang, X., Shen, J., Wang, L., Zhang, B., Zhang, M., Zhang, X., Zhang, C., & Li, M. (2014). A gut microbiota-targeted dietary intervention for amelioration of chronic inflammation underlying metabolic syndrome. FEMS Microbiology Ecology, 87(2), 357–367.

    Article  CAS  PubMed  Google Scholar 

  • Yatsunenko, T., Rey, F. E., Manary, M. J., Trehan, I., Dominguez-Bello, M. G., Contreras, M., Magris, M., Hidalgo, G., Baldassano, R. N., Anokhin, A. P., Heath, A. C., Warner, B., Reeder, J., Kuczynski, J., Caporaso, J. G., Lozupone, C. A., Lauber, C., Clemente, J. C., Knights, D., Knight, R., & Gordon, J. I. (2012). Human gut microbiome viewed across age and geography. Nature, 486(7402), 222.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zeevi, D., Korem, T., Zmora, N., Israeli, D., Rothschild, D., Weinberger, A., Ben-Yacov, O., Lador, D., Avnit-Sagi, T., Lotan-Pompan, M., Suez, J., Mahdi, J. A., Matot, E., Malka, G., Kosower, N., Rein, M., Zilberman-Schapira, G., Dohnalova, L., Pevsner-Fischer, M., Bikovsky, R., Halpern, Z., Elinav, E., & Segal, E. (2015). Personalized nutrition by prediction of glycemic responses. Cell, 163(5), 1079–1094.

    Article  CAS  PubMed  Google Scholar 

  • Zhernakova, A., Kurilshikov, A., Bonder, M. J., Tigchelaar, E. F., Schirmer, M., Vatanen, T., Mujagic, Z., Vila, A. V., Falony, G., & Vieira-Silva, S. (2016). Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity. Science, 352(6285), 565–569.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zoetendal, E. G., & de Vos, W. M. (2014). Effect of diet on the intestinal microbiota and its activity. Current Opinion in Gastroenterology, 30(2), 189–195.

    Article  CAS  PubMed  Google Scholar 

  • Zoetendal, E. G., von Wright, A., Vilpponen-Salmela, T., Ben-Amor, K., Akkermans, A. D., & de Vos, W. M. (2002). Mucosa-associated bacteria in the human gastrointestinal tract are uniformly distributed along the colon and differ from the community recovered from feces. Applied and Environmental Microbiology, 68(7), 3401–3407.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zoetendal, E. G., Raes, J., Van Den Bogert, B., Arumugam, M., Booijink, C. C., Troost, F. J., Bork, P., Wels, M., De Vos, W. M., & Kleerebezem, M. (2012). The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates. The ISME Journal, 6(7), 1415–1426.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

The research by Taojun Wang is financially supported by the China Scholarship Council (File No. 201600090211).

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Wang, T., Roest, D.I.M., Smidt, H., Zoetendal, E.G. (2019). “We Are What We Eat”: How Diet Impacts the Gut Microbiota in Adulthood. In: Azcarate-Peril, M., Arnold, R., Bruno-Bárcena, J. (eds) How Fermented Foods Feed a Healthy Gut Microbiota. Springer, Cham. https://doi.org/10.1007/978-3-030-28737-5_11

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